A few months back, two puffy, red eyes full of goop landed my toddler in the doctor’s office, where an exam also turned up two ear infections. This double-eye, double-ear whammy led to her first dose of antibiotics, post haste.

I was tremendously thankful for something that might make her feel better. But as she began slurping down her bubble gum-flavored medicine after breakfast, I worried for the fate of the billions of mostly helpful bugs in her body.

Scientists now know that the bacteria that live in and on us, called the microbiome, are important for our health in a huge number of ways. And those good bugs can be collateral damage in the war waged by antibiotics. That concern has been one of the motivations behind microbiologist and physician Martin Blaser’s research.

“Ten years ago I thought, ‘If farmers are using antibiotics to change the development of young animals, what are we doing to our kids?’” says Blaser, of the New York University School of Medicine. In 2012 and 2014, he and his colleagues published work showing that chronic, low doses of antibiotics increase body weight and change the microbiomes of young mice. Those results were worrisome, but the experiment looked at long-term, low exposure to antibiotics, a situation that’s different from what a kid might experience during an illness.

In their latest work, Blaser and colleagues tested shorter, higher doses of two kinds of antibiotics, similar to what a child might get for an ear infection. One was amoxicillin, the most commonly used antibiotic during childhood the world over, Blaser says. The second was tylosin, an antibiotic not used in people but of the same class as the ever-popular and convenient Z-Pak.

The mice received three courses of either antibiotic, a combination of the two, or neither early in their life. Animals that received either of the antibiotics weighed more and had larger bones, and also had long-lasting changes in their guts’ microbiome, the team reported June 30 in Nature Communications. The mice had their last dose of antibiotics on day 39 of life. Effects on their microbiome were still present 96 days later. Tylosin had stronger effects on the microbiome than amoxicillin, the team found.

Scientists are now trying to figure out the consequences of these bacterial changes. The results are in mice, not kids. It’s not clear how antibiotics early in life affect a growing child, but one thing is clear: Whatever the drugs are doing, they’re doing it to a lot of kids. By the age of two, the average child in the U.S. gets three rounds of antibiotics, Blaser says. That grows to 10 rounds by age 10.

Until we know more about the unintended consequences of antibiotics, people — especially doctors and parents — ought to be aware that they come with potential downsides. “Taking antibiotics has a cost,” Blaser says. “And cost has to be factored into the decisions.”

That’s a message that public health officials have been trying to get across in an effort to lower people’s exposure to unnecessary antibiotics. That goal is important for not just individuals, but society at large: Antibiotic overuse contributes to the growth of superbugs, bacteria that can do end-runs around our current antibiotics.

Rates of antibiotic prescriptions vary tremendously by region, infectious disease pediatrician Louise Vaz of Oregon Health & Science University in Portland and colleagues have found. And while antibiotic use had been declining over the last 20 years or so, it has leveled off recently, suggesting that there are still more improvements to be made in reducing exposure to needless antibiotics.

It turns out that lots of parents have misguided ideas about what symptoms require antibiotics, a knowledge gap revealed by a pop quiz that Vaz and colleagues gave parents. In the survey, less than half of the parents knew that bronchitis or a deep cough almost never needed antibiotics, the researchers reported July 20 in Pediatrics. Lots of parents also thought that green snot or a runny nose warranted the drugs. Those can be symptoms of common colds, flu and other illnesses caused by viruses. Viral infections most definitely bring misery, but antibiotics just don’t help.

Fear of antibiotic overuse shouldn’t keep the drugs away from a kid with a bacterial infection, though. “If a child is severely ill, of course he should be given antibiotics,” Blaser says. But the call often isn’t so easy. “There is a lot of gray,” he says. So when doctors and parents are deciding on treatment, it’s important to remember that antibiotics aren’t necessarily harmless.

That thought has been dogging me ever since my daughter recovered from her infection, only to pass her goopy eyes, congestion and fever on to the rest of us. After visiting all of our individual doctors, we’re all pretty sure it was a virus, no antibiotics needed.

Babies whose eighth month of gestation fell during the 2008 Beijing Olympics were born slightly heavier than babies born a year earlier or later, a stark indication of the effects of pollution on development.